Showing : genomicfeatures • reset
4
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9
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2.9k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 10 months ago by ★ 3.4k • written 11 months ago by ▴ 20
0
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3
replies
658
views
How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker GenomicScores phastCons100way.UCSC.hg38 GenomicFeatures
12 months ago rania.alanany • 0
3
votes
3
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815
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ISO a solution to rank-order introns by transcript
GenomicRanges GenomicFeatures
14 months ago • updated 11 months ago mat149 ▴ 80
0
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2
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1.0k
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
written 21 months ago by ▴ 10
2
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1
reply
1.4k
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Txdb object for UCSC hs1 (T2T-CHM13)
T2T-CHM13 GenomicFeatures
updated 23 months ago by 68k • written 23 months ago by • 0
0
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1
reply
1.3k
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.1 years ago rohitsatyam102 ▴ 20
2
votes
3
replies
4.8k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 2.2 years ago by 53k • written 2.2 years ago by • 0
2
votes
2
replies
1.1k
views
Few genes/transcripts in canFam (dog) TxDbs
TxDb.Cfamiliaris.UCSC.canFam4.refGene GenomicFeatures
2.3 years ago Geert ▴ 10
0
votes
2
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1.9k
views
What GENCODE GFF file for calculating exon length for TPM
GenomicFeatures
2.4 years ago gernophil • 0
1
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4
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1.3k
views
Submitting BSgenome package for a new assembly
bsgenome GenomicFeatures package
updated 2.5 years ago by 16k • written 2.5 years ago by • 0
1
vote
0
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902
views
Make custom Txdb class objects from Txdb
GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene
2.6 years ago Shreyash ▴ 10
4
votes
8
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3.0k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
2.7 years ago davidhillis • 0
0
votes
2
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1.6k
views
how to match salmon output to txname
GenomicFeatures tximport salmon
written 2.9 years ago by • 0
0
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5
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1.9k
views
Build custom TxDb Package using makeTxDbPackage
GenomicFeatures
updated 3.0 years ago by 68k • written 3.0 years ago by • 0
0
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0
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880
views
Mapping transcript to genomic positions via GenomicFeatures is not splice aware
GenomicFeatures
3.1 years ago nattzy94 ▴ 20
0
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2
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1.8k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.2 years ago by 43k • written 3.2 years ago by ▴ 10
0
votes
4
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3.1k
views
error with: .make_splicings <- function(exons, cds, stop_codons=NULL)
GenomicFeatures
updated 3.5 years ago by 16k • written 3.5 years ago by • 0
5
votes
9
replies
2.5k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 3.3 years ago by 43k • written 3.6 years ago by • 0
0
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18
replies
5.7k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.8 years ago • updated 3.7 years ago rbenel ▴ 50
3
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3
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2.1k
views
GenomicFeatures::makeTxDbFromUCSC failing with an error: identical(current_classes, .UCSC_TXCOL2CLASS) is not TRUE
genomicfea GenomicFeatures
updated 3.6 years ago by 68k • written 3.9 years ago by ▴ 30
1
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2
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2.0k
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How GenomicFeatures cdsBy() accounts for the frame info in the gff to get the CDS?
GenomicFeatures Biostrings
4.0 years ago Madza Farias-Virgens • 0
2
votes
3
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3.9k
views
How to get longest isoform
GenomicFeatures Biostrings
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
1
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2
replies
1.6k
views
NAs in my txdb tx_name
GenomicFeatures Biostrings
4.0 years ago Madza Farias-Virgens • 0
2
votes
2
replies
1.3k
views
Why `downstream` is set to 200 in the `GenomicFeatures::promoters` function
GenomicFeatures
updated 4.0 years ago by 16k • written 4.0 years ago by • 0
5
votes
2
replies
1.7k
views
How to build a GRangesList where each GRanges element is a CDS coordinate of gene transcripts?
GenomicRanges sesame sesameData GenomicFeatures
4.2 years ago Pratik Mehta ▴ 10
0
votes
1
reply
1.8k
views
install GenomicFeatures fail
GenomicFeatures install
updated 4.3 years ago by 68k • written 4.3 years ago by ▴ 80
1
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4
replies
2.2k
views
Is there anyway to replace seqlevels in a txdb
GenomicFeatures
4.3 years ago A.J. ▴ 20
1
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3
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1.7k
views
Can't produce a generegiontrack from my txdb anymore
gviz GenomicFeatures
4.3 years ago A.J. ▴ 20
1
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0
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1.6k
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DEXseq: How to do differential exon usage of genes with overlapping exons
GenomicFeatures DEXSeq
4.3 years ago Matthias Munz ▴ 20
0
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0
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1.2k
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annotatr with custom TxDb
GenomicFeatures annotatr genomicFe
4.6 years ago António Miguel de Jesus Domingues ▴ 510
0
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5
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3.8k
views
Genomic Features error in TxDbfromGFF
GenomicFeatures TxDb
4.7 years ago sieminsk • 0
2
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2
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2.2k
views
makeTxDbFromUCSC("mm10", "refGene") gives "not supported" error
GenomicF GenomicFeatures
4.8 years ago erhoppe • 0
0
votes
6
replies
1.9k
views
Splitting TxDb by Strand
GenomicFeatures TxDb
4.8 years ago rproendo ▴ 30
0
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3
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1.7k
views
Revisiting gene name inclusion in TxDB
Bioconductor GenomicFeatures TxDB
updated 4.1 years ago by • 0 • written 5.1 years ago by ▴ 120
0
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2
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4.3k
views
Why counts to tpm gives different values compared to tpm from kallisto?
rnaseq counts tpm GenomicFeatures kallisto
updated 5.1 years ago by 43k • written 5.1 years ago by • 0
0
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1
reply
1.0k
views
pmapToTranscripts for alternative isoforms
GenomicFeatures
updated 4.8 years ago by ▴ 80 • written 5.1 years ago by ▴ 10
0
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1
reply
5.9k
views
Add gene symbol when making TxDb
txdb genomicfeatures
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 90
3
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7
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2.2k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 5.3 years ago by 68k • written 5.3 years ago by ▴ 30
0
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1
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1.8k
views
error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 5.3 years ago by 4.2k • written 5.3 years ago by • 0
3
votes
6
replies
3.1k
views
TxDb, GenomicFeatures load from GTF file (Mmul_8)
TxDb GenomicFeatures
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 120
0
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1
reply
1.8k
views
makeTxDbFromGFF warning meaning
GenomicFeatures
updated 5.5 years ago by 68k • written 5.5 years ago by ▴ 100
0
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2
replies
1.5k
views
How to create GRanges for TES
GenomicFeatures TxDb CLIP-Seq
updated 5.5 years ago by ★ 11k • written 5.5 years ago by ▴ 10
0
votes
0
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1.3k
views
A warning : stop codons that cannot be mapped to an exon in using makeTxDbFromGFF
genomicranges genomicfeatures
5.6 years ago Guandong Shang ▴ 40
0
votes
2
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1.2k
views
Error with makeTxDbFromBiomart
GenomicFeatures
updated 5.6 years ago by 68k • written 5.6 years ago by ▴ 40
2
votes
3
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2.4k
views
Error "cannot map the following UCSC seqlevel(s) to an NCBI seqlevel" in package GenomeDbInfo
genomeinfodb hg19 ucsc seqlevel genomicfeatures
updated 5.7 years ago by 68k • written 5.7 years ago by ▴ 100
3
votes
4
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1.6k
views
how to close the recognizes features of type miRNA in "makeTxDbFromGFF"
GenomicFeatures genomicranges
updated 5.7 years ago by 16k • written 5.7 years ago by ▴ 40
1
vote
2
replies
1.3k
views
Any possibility to "cache" TxDb object?
GenomicFeatures TxDb
updated 5.7 years ago by ★ 13k • written 5.7 years ago by ▴ 40
0
votes
0
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1.4k
views
Error in trying to convert a gff file -> txdb object using GenomicFeatures::makeTxDbFromGFF()
GenomicFeatures annotation gff GenomicRanges
updated 5.8 years ago by 4.2k • written 5.8 years ago by • 0
0
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2
replies
1.3k
views
biomart webservice error during makeTxDbFromBiomart in r package GenomicFeatures
biomart txdb makeTxDbFromBiomart GenomicFeatures
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
8
votes
12
replies
7.0k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 3.4 years ago by • 0 • written 10.7 years ago by ▴ 20
291 results • Page 1 of 6
Recent ...
Replies
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Answer: p.adjust BH Question by Gordon Smyth 53k
Duplicate of https://support.bioconductor.org/p/41077/
Answer: Large logFC but somewhat high FDR by Gordon Smyth 53k
Glad you're getting good use out of the package. The results that you show seem pretty much as one would expect, with nothing surprising. …
Votes
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
A: p.adjust BH generates duplicate values
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